We assessed the vertical variation of bacterial abundance, diversity and community composition in deep, high-altitude (4730 m above sea level) Lake Nam Co. The bacterial abundance reduced with increasing depth, while bacterial diversity increased in the deeper bottom water. Pyrosequencing revealed that the bacterial community in the lake showed a pronounced vertical shift: the Bacteroidetes and Proteobacteria had relatively higher abundance in the epilimnion and metalimnion; the Firmicutes group dominated in the metalimnion; the Actinobacteria and Cyanobacteria mainly occupied the metalimnion and hypolimnion. Water temperature, conductivity, photosynthetically active radiation, and chlorophyll a were significantly correlated with the bacterial communities. These results indicated that the bacterial communities appeared to have an apparent vertical structure under lake stratification.